Humans Not Machines
by RX105STRIKE
Summary: They were once best friends until they came. They stole his future, his family, and his friend Houki. Forced into a different universe he fought against the Insurrectionists and later the Covenant. After 27 years of fighting he forgot about his childhood, but when Cortona opens a prototype waypoint, in order to save his life, he is finally back home. (check profile for updates)
1. The Promise (prologue part 1)

**AN: I do not own Halo or Infinite Stratos. They belong to their rightful owners.**

**Also please add some feedback. ENJOY!**

10 years ago

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"John wait up!" cried a small little girl with a green ribbon tied to her ponytail

John starts to snicker as he sees his friend trying hard to catch up.

"C'mon Houki we are almost there."

The reason why John is so excited today is because a couple days ago he discovered an amazing place up on a cliff and he wants to show Houki his discovery.

Houki soon begins to pant, forcing herself to stop, " *Huff *Huff why are we hiking on a steep cliff again?" she asks tiredly

"You'll see," John said happily. He looks at his friend and realizes he may have pushed Houki at her limit. She leans on a rock covered in sweat panting heavily as if she ran an Olympic Marathon. "Hmmmm, you tired?" John felt a little guilty for pushing his friend a little too far. Only he is wearing proper clothes for a proper hike: a comfortable blue shirt, short pants, and a pair of black running shoes. Houki on the other hand is wearing a traditional white kimono and pair of traditional Japanese wooden sandals. John sweat drops realizing Houki's sense of fashion is not right for a steep hike like this.

Houki stops panting and looks at him with a raised eyebrow. " Who me? Nah I'm alright!" Houki said quickly, trying to not look weak and feeble in front of her friend. However she had to face the fact that she doesn't have the endurance like John and she could feel blisters on her feet start to form.

Noticing his friend rubbing her feet tenderly, John sighed a little and walks slowly towards Houki and kneeled with his back turned. "John-kun what are you doing?"

He sighs once more, "Climb on my back." This startles Houki and she quickly hid her blush with her long sleeves.

"B-b-but Tabanee-neesan will think the wrong way or... or our parents might think that w-w-we are a couple." She said hesitantly. Just thinking of her older sister and their parents gave her cold shivers if they see her and John having this kind of close relationship.

John laughs at her remark. " Relax Houki, you are clearly tired. If our parents pop up we can always make an excuse, just climb on."

She sighs and agrees to have a piggyback on John. As Houki climbs onto John, her face turns red as a tomato. Once she climbs on John, he starts to stand and Houki is amazed of how much she could see while on John's back.

"Wow John!" I can see the beach from here!" Houki was actually enjoying herself riding on top of John. All what John can do is sigh and smile at his friend for having a fun time riding on his back.

After five minutes of hiking, the two kids finally reach the top of the cliff and Houki's mouth drops in awe. On top of the cliff the ground is covered with lush grass with a variety of colorful flowers, and in the center, a huge banzai tree. Not only did this cliff amaze Houki but the ocean across the cliff as well. Soft light from the sun seems to add liveliness to the ocean giving it a bright sky color.

Houki is mesmerized at this landscape but her daydreaming is quickly interrupted. " Ta da! This is my surprise Houki"

Houki's mouth drops again with excitement and she jumps off of John's back and runs towards the banzai tree. " This place is beautiful John, it was worth the hike.

John sweat drops at her remark. " I did most of the work though." He mutters

"What was that John?"

John waves both of his hands at Houki, " Nothing Nothing heh heh."

Houki raises an eyebrow but she quickly shook her head and starts to twirl and dance on the flowerbed.

John starts to get nervous at Houki's carelessness for ignoring her surroundings because she is dancing and twirling near the edge of the cliff.

"Houki!" He said nervously, " be careful, you're dancing near the edge."

Still dancing and twirling, Houki ignores his warning. Still twirling, " Relax John. I'm not going to—" She trips on a small pebble and starts to lose her balance non the edge of the cliff. " John...heelll...HELP ME!" she cries while trying to balance herself

Before she completely fell, John quickly grabs her arm and pulls her towards him. The sudden force and Houki's weight also made John lose his balance and his back quickly hits the rocky ground while his chest protects Houki from the fall."

Houki is the first to get up and she quickly rubs her head, " Ow...Ow...that's going to leave a mark. " After her head clears up she opens her eyes and is shocked that she is on John chest. She jumps off of John and crawls to his side, " John are you alright."

"Ow, I'm...I'm alright" Houki sighs with relief but her eyes widens when she see's his right arm bleeding.

"John!" She screams," "Your...Your Arm!"

"Wha—oh" He inspects the wound, " It's alright Houki tis but a scratch." He said jokingly. Suddenly, John feels something wet on his hands. When he looks at them he sees small droplets of water on them. He looks at Houki and his eyes slightly widens as Houki is crying.

"Hey, hey! Why are you crying" he whispers

"It's...*Sniff...It's my fault your hurt because of me." She said sadly as she is trying to wipe all the tears off of her eyes.

Thinking their friendship is over, Houki shuts her eyes and begins to tense preparing herself if John wants to slap her for hurting him, but instead she feels a couple small pats on her head. As she slowly opens her eyes she sees John still smiling.

Houki is...speechless. It is her fault that John is hurt and yet he is still smiling. The thought of his kindness made her cry again. Still trying to rub all the tears off, Hoiki suddenly buries her head on his chest. Still on the ground John has difficulties sitting up due to Houki still hugging his chest. " I am not worthy of such kindness John!" She cried. Even though it is quite cheesy John didn't care. Still burying her head, John can feel his shirt slowly becoming soaked with tears. " I...I don't know why I'm crying still" she mutters, " will...will you forgive me?" She weakly asks.

John is speechless of Houki still feeling guilty but she quickly smiles and pats her hair once again. He sighs, " Of course silly, I forgive you, just... try to be more careful okay." Houki silently nods her buried head.

After the accident, Houki stops crying and the two "carefully" play together until the sun starts to set.

Beneath the huge Banzai tree, the two friends are making flower crowns from the flowers nearby. Houki finishes her crown first and smiles at her hardwork. She takes a quick peak at John and she see's her friend having trouble making the knots on his crown. She giggles at her friend and slowly looks at the horizon watching the sun starting to set.

She sighs, " Another day gone."

John looks at the horizon for a second then looks back at his completed flower crown. He gave a quick smirk of his first flower crown and places it on Houki's head while she is distracted. " There, now you look like princess" he said energetically.

Houki blushes and looks away but before he could protest she realizes John's right arm is getting worse. " John your arm is getting worse!" She said nervously. Houki starts to crawl towards his arm for a better inspection. Even though the blood is gone, the wound is swelling. After inspecting his arm, even though Jon begs her to drop the subject, Houki starts to feel guilty even more. " It's my fault he's injured." She mentally said.

Then an idea hit her. She quickly gets up and began to untie her ribbon off . After untying her hair, she used her ribbon as a makeshift band-aid.

"Houki wait!" John said as Houki wraps her ribbon on his wound. After she is done, John didn't know what to say. He slowly looks at the makeshift Band-Aid then slowly turns his head at Houki. " Houki... isn't this your favorite ribbon?" she asks quietly.

Houki blushes yet again and starts to play with her hair, " Yeah but... it's just a ribbon, you are worth more than any stupid ribbon my mom gives me."

John didn't know what to say. He looks back at his covered wound then smiles back at Houki," Thank you Houki, for having such a big heart on a foreign guy like me."

"Well... don't mention it she said hesitantly." Seeing that the sun is almost gone Houki starts to believe it is time to go back to their parents. " Hey John, I think it's time to go home now. We can come back tomorrow and play."

John's smile began to fade and he looks down at the flowers looking guilty and sad.

What's wrong John?" She asks nervously.

"Today will be the last day for us to see each other for a while," he said sadly

Houki eyes grew wider. " What... why!?" She choked

He sighs once more," Father's company is having issues so we have to go back to the homeland to repair all the damages.

The truth is that John's dad, Ron Hunter, is CEO of APEX. A corporation that manufactures the United States 1st Gen IS. Ron had to go back to the United States because his competitor, the Dunois Corporations, has been selling 1st Gen ISs with lighting speed causing APEXs stocks to rapidly decrease.

"Don't worry Houki." John said caringly. "" It's just a business trip. We will be back in a month okay."

"A MONTH!" She shouted, " What will I do in 30 days without a friend like you." She looks down at her toes fighting the urge to cry. " I already lost a friend I don't want to lose another dear friend" She looks up at him with red eyes and shows him her pinkie. " Pinkie promise me you'll come back."

"...Houki"

"Just... come back... I will be waiting for you here... okay?

"You know I hate goodbyes." He said sadly, " But I promise." He locks his pinkie finger with hers as a childhood promise he swears to keep.

However...this will be the last time these two childhood friends will ever see each other.

...for now.


	2. Tying Up Loose Ends ( prologue part 2)

**I DO NOT OWN INFINITE STRATOS NOR HALO. THEY BELONG TO THEIR RIGHTFUL OWNERS.**

**HI GUYZ I'M BACK! Sorry for the long wait. I had so much homework and tests I literally had no time writing. Thank you for everyone's support, it really means alot to me. I never knew my story was that popular. Also please push that review button. I love reading your comments and I will try to implement some of your ideas into my story if possible. Please feel free to ask any questions, concerns, or some praises :3 lol. Don't worry you guys becasue this will be the last chapter for the prolouge. Next chapeter will be the real deal :). Speaking of future chapters, expect new chapters every month. I will update my progress on my profile every Friday.**

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Present Day

It has been 6 days since John had received his augmentations and for 6 days straight, he couldn't sleep. Every night he would receive these weird dreams about these so called ISs, the Hunter family, and a little girl named Houki. At first he thought it was a weird dream but every night, these images became even more vivid.

John tosses and turns on his bed, trying to get comfortable but failed to. He throws his blanket off and sits up upright, hugging his legs.

"What the hell do they mean?"he whispers.

Reaching under his pillow, he grabs a green ribbon, which he has kept safe from the councilors and Halsey. To John, this green ribbon he cherishes is the only connection with his past life. Even though he does not remember much about his past, he can only remember that his mother smelled like soap and his father was always proud of him. But, there was no memory of this girl named Houki. However, John is skeptical because the girl in his dreams was also wearing the same green ribbon he is holding...maybe a coincidence?

Hearing his door open, John quickly hides the green ribbon under his pillow and looks up to the newcomer.

"John, are you alright?"

John starts to smile a little, knowing that the stranger is Halsey.

"Yes Halsey... I'm alright."

Halsey gives him a sympathetic look, grabs a chair near the door, and sits near John's bed.

"I hear that you are having trouble sleeping John."

John hugs his legs tighter, knowing that she wants an explanation for what's happening to him.

"Yeah... but I'm alright."

Halsey raises an eyebrow, knowing that John was hiding something from her.

"You wanna tell me?"

"Well you wouldn't believe me Halsey"

"Try me."

John sighs and hugs his legs even tighter. "Well I am having these dreams about a girl."

Halsey raises her eyebrow. "A girl? Hmmmm... please...continue."

Halsey is a little skeptical about John's dreams because his augmentations should have suppressed his sexual desires to begin with. Oh well... it's common for a 15 year old to have a sexual need so Halsey ignored it.

"Well there are these mecha piloted by only females...I think they are called Infinite Stratos. Then this girl and I and for some reason we were hiking on this cliff."John starts to rub his head with frustration. "And somehow it felt like I have been there before"

Halsey squints her eyes knowing the cause of John's sleeping problems. "Anything else John? Like do you know her name?"

"Yeah... her name is... Houki Shinnono."

Halsey secretly clenches her hand really hard, "... oh... I see."Knowing that John is treading into dangerous water Halsey quickly tries to change the subject, "Well John it's just a dream so don't be so preoccupied with visions that have no meaning. Tell me John what are you?"

John quickly releases his legs and looks at Halsey with a stoic expression, "I am a SPARTAN Ma'am."

"Tell me SPARTAN what is your object?"

"To neutralize all threats that is threatening Earth and her colonies."

"Do you believe that these dreams are prohibiting your objective?"

"Ye-ye..."he sighs, "yes ma'am."

Halsey's soon smiles and pats John's shoulder, "you should sleep now John your body is still adjusting from the augmentations."

John nods and slowly reclines back onto his bed. Outside of John's room Halsey reaches into her lab coat pocket and grabs her communicator and pushes sets of keys.

"Put me on the line of the Director of ONI Sector III ...NOW!."

In Halsey's room, Halsey's is staring at a computer screen with impatient sets of tapping coming from her fingers. Right now, she is waiting for the Director to respond back to her calls. After 30 minutes of waiting impatiently, her computer starts to ring.

As the computer springs to life, a skinny man wearing a business suit is shown. He has short brown hair, wearing huge set of glasses, and a huge scar that connected from his left ear to his lower left mouth. On the bottom left corner of the screen, the man's name is Director Drake.

Director Drake smiles at Halsey, "Ah Dr. Halsey, I didn't expect you to contact me until a week later, how are my products doing so far?"

"Your 'products' are doing fine Director however, I am not here to tell you that they are combat ready yet."

Director Drake squints and his lips starts to twitch,"Explain."

"Well as you may know only 33 survived the augmentation and I need at least 1 month or 2 for them to adjust to their new bodies,"Halsey said stoically.

Drake laughs at Halsey's excuse, "GAHAHAHA that's a good one Halsey, I never knew you were a comedian. His laughter soon transforms into anger,"and yet you have the audacity to tell me that you want to extend your deployment quota right after I gave you the numerous funding for your little SPARTAN augmentations and their armor.

Halsey clenched her knuckles yet again. "Director my Spartans are humanities next step in evolu-"

Drake cuts her off, "OH SPARE ME OF THAT EVOLUTION CRAP CATHERINE! The UNSC is literally breathing behind my back!" Drake starts to hastily pull his tie in order for him to breathe easily. "The Insurrectionists are getting bolder and bolder each day Catherine we need your SPARTANs on the battlefield ASAP!"

Halsey rolls her eyebrows knowing the situation too well, "I know that Director but I mostly concerned with Sierra 117."

This caught the Director's attention as he reclined back into his chair and fixing his tie calmly, "and why are you so concerned with the boy from Project COLUMBUS?"

Project COLUMBUS was top-secret program that involved with the UNSCs top physicists to research if an alternate reality existed. Knowing that the SHAWFUJIKAWA SlipSpace Drive takes ships into the multiverse, UNSC scientists theorize that isolating a specific dimension in a SlipSpace Drive would safely allow anyone to enter an alternate world rather than "teleporting" from one point to another. On August 17, 2517, mankind finally took it's first step into a different reality. That was also the day Catherine volunteered into the program and found John.

"I believe that the serum you gave me 10 years ago has finally worn off."

The serum Halsey injected into John 10 years ago was an illegal ONI military grade drug that was designed to erase the long-term memories of the patient then forces the subject with false memories in order to make obedient soldiers. This was supposed to be used for conscripting more soldiers from the public if ever the Top Brass requested it. however since it infringed human rights, manufacturing them was kept secret.

Drake snorts, "Then give him another one."

Halsey rolls her eyes and shakes her head, "Director, if I knew a solution like that would be simple, I wouldn't have this meeting to begin with."

"Why won't it work?"

"It's his Superconducting Fibrification Neural Dendrites augmentation that's causing it."

Right now his "new body" is rejecting the drug causing him to have sudden flashbacks of his old memories in his dreams.

"Then what do you want to do?"

"All I want is one more month before we launch the SPARTANs. I need time to convince him that his old memories are all but dreams and delusions then we can relax."

The director is still not convinced and scratches his head, "I don't know Catherine, that is kind of risky for me to tell the Brass to postpone the SPARTAN deployment till next month."

Halsey sighs, "Drake think about it. Do you want a rogue SPARTAN killing everything in his path in order to find a girl that's not from this world? Knowing you and rest of ONI, that would be very costly to terminate him."

Drake rolls his eyes and surrenders to Halsey. "Alright-alright you win Halsey. But remember, these SPARTANs are equivalent to a battle group. I invested a lot so if I see you or your SPARTANs mess up then I won't save you if the rest of ONI discovers your crimes."

Halsey clenches her fist at his remark. "Fine... it's a deal."

Still can't sleep, John throws his blanket off of him. These dreams are driving him insane. He needs answers and the only place that has all of his questions is the ONI data mainframe in one of their computer terminals. After tying his shoes, John quickly grabs his green ribbon underneath his pillow, stashed it in his pocket, and began to silently walk of outside his room, searching for the nearest computer terminal. After about 20 minutes of silently walking from corridor to corridor, John finally found a computer terminal.

After activating the computer terminal the UNSC logo appeared on the screen. Before John could type anything Deja's hologram appeared near John.

Deja swipes her hand and instantly, a small probe, materializes near him. Then the small probe shoots a blue horizontal beam and rapidly starts to scan him, in order to identify who is the intruder.

_"Scan complete,"_said the probe, "_Identity confirm to be Sierra 117._"

"Warning, you are not authorized to use this terminal during curfew hours SPARTAN 117."Said Deja.

"Deja I need your help."

"And why would you need my assistance? You know it is past curfew 117."

"I know... but I need some answers and I believe you are the quickest way for me to get them."

Deja is still not convinced and she waves her right hand. Series of words soon appears before her and the word security materializes. Before she could warn security John stops her.

"Wait Deja!"

Deja stops herself,"What is it 117, this is for your own good."

"I know but I am afraid that if I say something, the Councilors would think that I have gone insane... please Deja I need your help."

After all these years of teaching John, Deja felt something in her "mind" that is not part of her primary program. It was sympathy.

"Acknowledged...however, this will be the only time I will assist you 117; the next time you break protocol I will contact the nearest security personnel."

John smiles, "okay, it is a deal"

"What is it that you require assistance?"

"Can you search for my background Deja?"

"I am sorry 117 but my programming is only designed to teach you SPARTANs military stratagems and core education, not data retrieval."

John silently curses himself for forgetting that Deja is a dumb AI.

"However... I do have files of each SPARTAN from Halsey 117."

John's eyes widen and felt excitement building in his stomach.

"Really! Can you look at my file please Deja."

"Affirmative."

Deja activates the terminal and bunch of files referring to John pops up. He sighs knowing that his answers will finally be answered.

"Alright, Deja where is my home planet?"

"You were born on Eridanus."

"Okay... what city?"

"Elysium II."

"Hmmm... have I ever been on Earth before?"

Deja starts to search the UNSC civilian transport records and SlipSpace traffic records if John or his family has ever traveled off world.

"According to the flight records...negative."

He bites his lips and scratches his head with frustration.

He sighs with irritation, "Okay... are you programmed to search non-military military personnel?"

"Affirmative... however I never searched anyone that is beyond the UNSC military forces because my primary programming was to educate you and your SPARTANs preparations for your career."

"Alright... can you search for a teenage Japanese girl. She probably the same age as me."

"Name?"

John grabs the green ribbon out of his pocket and stares at it with a small smile.

"Her name is Houki Shinnono."

"Do you know which planet she is on?"

"I believe she is on Earth, somewhere in Japan."

Deja inputs Houki's name and a couple seconds later the results finally came in.

"I am sorry 117 however she does not exist in my records."

John suddenly starts to panic.

"Wha-what! Deja, try again!"

Deja waves her hand and series of numbers and names appears. After thoroughly searching for her name, Deja looks at John and slowly shakes her head.

"I am sorry 117 she does not exist."

John could feel tears in his eyes streaming down on his cheeks and his legs weak from shock. Giving into his shock, he collapses on his hands and knees.

"Spartan 117, this behavior is quite bizarre."

"I...I know Deja,"John whispers,"but... I don't know why this girl is in my head so vividly."

"It is probably due to your augmentations 117. Your brain is probably fooling yourself. Please... do not cry... it is strange to me to see a soldier crying especially you 117."

John wipes his tears on his sleeves vigorously and slowly walks back into the shadows.

"Where are you going 117?"

Sadly John has to give into what Halsey and Deja's reasoning. He would have to accept that these are but mere dreams and nothing more.

John looks at Deja with teary eyes and said, "I'm going to bed Deja... like you said... it is past curfew."

1 month after the incident

Today has finally come for John because today is the day he and his squad will be finally be deployed to the outer colonies. In the armory, some Spartans are fitting into their Mk IV suits. Numerous metal appendages assemble each Spartans' limbs of armor piece by piece. The rest of the Spartans are outside of the armory waiting for their turn.

"117 you are up," said one of the staff.

John marches inside of the armory towards his armor. As John walks up the pedestal with his arms raised horizontally a staff looks at John's hand with curiosity. By examining it carefully he realizes that John is holding a green ribbon.

"Um 117, what is that you are holding?"

Ignoring the staff, John carefully ties the green ribbon to his right arm then resumes lifting his arms horizontally waiting to be assembled.

All of the scientists are baffled at John's behavior. "Um...okay?"said one of the scientists. Shaking his head the scientist starts to assemble the torso piece onto John. The noise from the appendage wakes the entire staff and everyone starts to piece the armor onto John. First, the torso connects to John. Then, his thigh pieces carefully encase his undersuit. Afterwards, four new appendages encase his arms, securing him tightly. Lastly, came his shoulder pads. The left one was attached to his body first as the scientists made sure that it fit snugly onto John. Finally his right shoulder pad is aligned on John's shoulder. Slowly the shoulder pad magnetically locked onto John's shoulder covering the green ribbon from plain sight. Before the scientists puts John's helmet on his head the scientists starts to examine each piece of his armor to make sure there are aligned properly.

"Okay 117 do you feel any discomfort or anything out of the ordinary?"

John stoically shakes his head.

As if on cue, his helmet slowly descends from the ceiling and carefully attaches on his head. John's hud sprang back to life as he sees each scientist examining his suit for the last time before he is deployed on the front lines. Once the scientist gives John the thumbs up, he slowly starts to walk off the pedestal and casually into the waiting Pelican where most of his brothers are waiting eagerly for departure.

"Hey John, you excited to kick some insurrectionists' ass with these suits. I feel like I can take down Indies with my bare hands!"said an eager SPARTAN. John slowly looks at the SPARTAN and nods.

Most of his brothers and sisters are excited to finally test their suit in an actual firefight, except for John. He still has this feeling as if someone is waiting for him back home.

...He is right about that.


End file.
